The Nielsen Lab has developed several software packages including:
Analyses of Next Generation Sequencing Data. Our new program package for analyzing NGS data developed by Thorfinn Korneliusen with help from Anders Albrechtsen and others. Learn more here.
C/C++ programs to simulate NGS data, to compute estimates of FST, of the sample covariance matrix and of the 2D-SFS, by Matteo Fumagalli. Estimates of population genetics parameters are based on posterior probabilities of genotypes and sample allele frequencies as in Nielsen et al. 2012. Input files can be generated using the ANGSD software. Learn more here.
A program to estimate per-individual inbreeding coefficients by Filippe Vieira. Learn more here
It can be used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data. Learn more here.
Used for finding the ascertainment corrected frequency spectrum based on ascertained SNP data. Learn more here.
Program will allow the user to estimate selection coefficients relating to optimal codon usage. Learn more here.
A program for simulating samples in a codon based models under the coalescent with recombination. Learn more here.
(PaTeRnity Inference) A program for paternity analysis of genetic data. Learn more here.
IM and IMa
A program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). For most purposes you probably want to use one of the IM programs instead. Learn more here.
A phenomenal, and terribly underutilized, program developed by Anders Albrechtsen. It provides a very flexible method for association mapping for multifactorial traits in the presence of gene-gene and gene-environment interactions. I have really no idea why this method is not more used in association mapping studies – but I guess we can’t be too great at advertising. Learn more here.
A program for estimating the likelihood surface for theta (4 times the effective population size times the mutation rate) for population genetic microsatellite data. This program is old. There must be better methods out there. Learn more here.
Browse additional programs made available by the Center for Theoretical Evolutionary Genomics here.